[Dart-dev] DART/branches Revision: 10855

[dart at ucar.edu]

hendric at ucar.edu
2016-12-30 15:53:18 -0700 (Fri, 30 Dec 2016)
225
Commiting changes from Wednesdays file review.  Mostly
updating comments and changing variable and routine names.
In perfect model obs you must specify a restart in and
out file in order to run otherwise pmo will error out.




Modified: DART/branches/rma_fixed_filenames/filter/filter_mod.f90
===================================================================
--- DART/branches/rma_fixed_filenames/filter/filter_mod.f90	2016-12-30 17:21:03 UTC (rev 10854)
+++ DART/branches/rma_fixed_filenames/filter/filter_mod.f90	2016-12-30 22:53:18 UTC (rev 10855)
@@ -171,11 +171,11 @@
 logical            :: perturb_from_single_instance = .false.
 real(r8)           :: perturbation_amplitude       = 0.2_r8
 ! File options.  Single vs. Multiple.
-logical            :: single_file_in               = .false. ! all copies read from 1 file
+logical            :: single_file_in               = .false. ! all copies read  from 1 file
 logical            :: single_file_out              = .false. ! all copies written to 1 file
 ! Stages to write
 character(len=10)  :: stages_to_write(4) = (/"null      ", "null      ", "null      ", "output    "/) ! input, preassim, postassim, output
-logical :: output_restarts  = .true. !>@todo rename to output_members
+logical :: output_restarts  = .true. !>@todo rename to output_members?
 logical :: output_mean      = .true.
 logical :: output_sd        = .true.
 logical :: write_all_stages_at_end = .false.
@@ -188,22 +188,17 @@
 
 ! Inflation namelist entries follow, first entry for prior, second for posterior
 ! inf_flavor is 0:none, 1:obs space, 2: varying state space, 3: fixed state_space
-integer              :: inf_flavor(2)             = 0
+integer              :: inf_flavor(2)                  = 0
 logical              :: inf_initial_from_restart(2)    = .false.
 logical              :: inf_sd_initial_from_restart(2) = .false.
+logical              :: inf_deterministic(2)           = .true.
+real(r8)             :: inf_initial(2)                 = 1.0_r8
+real(r8)             :: inf_sd_initial(2)              = 0.0_r8
+real(r8)             :: inf_damping(2)                 = 1.0_r8
+real(r8)             :: inf_lower_bound(2)             = 1.0_r8
+real(r8)             :: inf_upper_bound(2)             = 1000000.0_r8
+real(r8)             :: inf_sd_lower_bound(2)          = 0.0_r8
 
-! new way
-!logical              :: inf_output_prior(2) = .false. ! mean sd
-!logical              :: inf_output_post(2)  = .false. ! mean sd
-
-logical              :: inf_deterministic(2)      = .true.
-real(r8)             :: inf_initial(2)            = 1.0_r8
-real(r8)             :: inf_sd_initial(2)         = 0.0_r8
-real(r8)             :: inf_damping(2)            = 1.0_r8
-real(r8)             :: inf_lower_bound(2)        = 1.0_r8
-real(r8)             :: inf_upper_bound(2)        = 1000000.0_r8
-real(r8)             :: inf_sd_lower_bound(2)     = 0.0_r8
-
 logical :: debug = .false.
 
 namelist /filter_nml/ async, adv_ens_command, ens_size, tasks_per_model_advance, &
@@ -636,7 +631,7 @@
    
    ! Write out the mean and sd for the input files if requested
    if (get_stage_to_write('input')) then
-      if (output_mean) call set_io_copy_flag(file_info_input, INPUT_MEAN, WRITE_COPY)
+      if (output_mean) call set_io_copy_flag(file_info_input, INPUT_MEAN, WRITE_COPY, has_units=.true.)
       if (output_sd)   call set_io_copy_flag(file_info_input, INPUT_SD,   WRITE_COPY, has_units=.false.)
       if (write_all_stages_at_end) then
          call store_input(state_ens_handle)
@@ -2219,12 +2214,10 @@
 do i = 1, nstages
    my_stage = stages(i)
    call to_upper(my_stage)
-   write(msgstring,*)" checking ", trim(my_stage)
-   call error_handler(E_MSG,'parse_stages_to_write',msgstring,source,revision,revdate)
    if (trim(my_stage) /= trim('NULL')) then
       call set_stage_to_write(stages(i),.true.)
       if (debug) then
-        write(msgstring,*)"PARSE STAGE "//trim(stages(i))//" TRUE"
+        write(msgstring,*)"filter will write stage : "//trim(stages(i))
         call error_handler(E_MSG,'parse_stages_to_write', &
                            msgstring,source,revision,revdate)
       endif

Modified: DART/branches/rma_fixed_filenames/io/direct_netcdf_mod.f90
===================================================================
--- DART/branches/rma_fixed_filenames/io/direct_netcdf_mod.f90	2016-12-30 17:21:03 UTC (rev 10854)
+++ DART/branches/rma_fixed_filenames/io/direct_netcdf_mod.f90	2016-12-30 22:53:18 UTC (rev 10855)
@@ -102,8 +102,6 @@
 character(len=32 ), parameter :: revision = "$Revision$"
 character(len=128), parameter :: revdate  = "$Date$"
 
-! Limit_mem is a namelist item in state_vector_io_mod.
-
 integer :: ret !< netcdf return code
 
 character(len=512) :: msgstring
@@ -193,10 +191,8 @@
    start_var = 1 ! read first variable first
 
    ! open netcdf file
-   ! print*, 'query_read_copy ', copy, query_read_copy(name_handle, copy)
    if (query_read_copy(name_handle, copy)) then
       netcdf_filename = get_restart_filename(name_handle, copy, domain)
-      ! print*, 'reading ', trim(netcdf_filename), copy, domain
       ret = nf90_open(netcdf_filename, NF90_NOWRITE, ncfile)
       call nc_check(ret, 'direct_netcdf_mod.f90 read_transpose_single_task: opening', netcdf_filename)
    endif
@@ -268,7 +264,6 @@
    start_var = 1 ! read first variable first
 
    ! open netcdf file